diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index be37211..58ca644 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/output.json b/output.json index 61f61bc..e04c786 100644 --- a/output.json +++ b/output.json @@ -10,61 +10,61 @@ {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 596, "status": "unchecked", "code": 0, "uri": "", "info": ""} {"filename": "open_science/Data-sharing.md", "lineno": 26, "status": "unchecked", "code": 0, "uri": "#licensing-target", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 238, "status": "unchecked", "code": 0, "uri": "#slurm-arguments-target", "info": ""} +{"filename": "open_science/Licensing.md", "lineno": 21, "status": "working", "code": 0, "uri": "https://choosealicense.com/", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 70, "status": "working", "code": 0, "uri": "https://conda.org/blog/2023-11-06-conda-23-10-0-release/", "info": ""} -{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 64, "status": "working", "code": 0, "uri": "https://sleap.ai/installation.html", "info": ""} -{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 73, "status": "working", "code": 0, "uri": "https://sleap.ai/installation.html#conda-package", "info": ""} {"filename": "programming/SSH-SWC-cluster.md", "lineno": 72, "status": "working", "code": 0, "uri": "https://code.visualstudio.com/", "info": ""} -{"filename": "open_science/Data-sharing.md", "lineno": 73, "status": "working", "code": 0, "uri": "https://crcns.org/", "info": ""} -{"filename": "open_science/Licensing.md", "lineno": 21, "status": "working", "code": 0, "uri": "https://choosealicense.com/", "info": ""} +{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 64, "status": "working", "code": 0, "uri": "https://sleap.ai/installation.html", "info": ""} {"filename": "open_science/Data-sharing.md", "lineno": 42, "status": "redirected", "code": 301, "uri": "http://www.brainimagelibrary.org/", "info": "https://www.brainimagelibrary.org/"} {"filename": "programming/Cookiecutter-cruft.md", "lineno": 3, "status": "working", "code": 0, "uri": "https://cruft.github.io/cruft/", "info": ""} -{"filename": "open_science/Data-sharing.md", "lineno": 43, "status": "working", "code": 0, "uri": "https://dandiarchive.org/", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 76, "status": "working", "code": 0, "uri": "http://ccdb.ucsd.edu/home", "info": ""} {"filename": "open_science/Data-sharing.md", "lineno": 28, "status": "working", "code": 0, "uri": "https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 43, "status": "working", "code": 0, "uri": "https://dandiarchive.org/", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 73, "status": "working", "code": 0, "uri": "https://crcns.org/", "info": ""} {"filename": "open_science/Data-sharing.md", "lineno": 63, "status": "redirected", "code": 301, "uri": "https://datadryad.org", "info": "https://datadryad.org/stash"} -{"filename": "open_science/Data-sharing.md", "lineno": 64, "status": "working", "code": 0, "uri": "https://gin.g-node.org/", "info": ""} -{"filename": "open_science/Data-sharing.md", "lineno": 74, "status": "working", "code": 0, "uri": "https://gin.g-node.org/BrainGlobe/atlases", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 37, "status": "working", "code": 0, "uri": "https://gin.g-node.org/SainsburyWellcomeCentre", "info": ""} {"filename": "programming/SSH-SWC-cluster.md", "lineno": 34, "status": "working", "code": 0, "uri": "https://gitforwindows.org/", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 74, "status": "working", "code": 0, "uri": "https://gin.g-node.org/BrainGlobe/atlases", "info": ""} {"filename": "open_science/Data-sharing.md", "lineno": 65, "status": "redirected", "code": 301, "uri": "https://ebrains.eu/service/share-data", "info": "https://www.ebrains.eu/data/share-data/"} -{"filename": "open_science/Data-sharing.md", "lineno": 37, "status": "working", "code": 0, "uri": "https://gin.g-node.org/SainsburyWellcomeCentre", "info": ""} -{"filename": "open_science/Data-sharing.md", "lineno": 26, "status": "working", "code": 0, "uri": "https://github.com/SainsburyWellcomeCentre", "info": ""} {"filename": "programming/Cookiecutter-cruft.md", "lineno": 3, "status": "working", "code": 0, "uri": "https://github.com/cruft/cruft", "info": ""} -{"filename": "programming/SSH-SWC-cluster.md", "lineno": 266, "status": "working", "code": 0, "uri": "https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh", "info": ""} -{"filename": "open_science/Data-sharing.md", "lineno": 49, "status": "working", "code": 0, "uri": "https://neuroblueprint.neuroinformatics.dev/", "info": ""} +{"filename": "open_science/Licensing.md", "lineno": 51, "status": "working", "code": 0, "uri": "https://joinup.ec.europa.eu/collection/eupl/solution/joinup-licensing-assistant/jla-compatibility-checker", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 26, "status": "working", "code": 0, "uri": "https://github.com/SainsburyWellcomeCentre", "info": ""} {"filename": "open_science/Data-sharing.md", "lineno": 71, "status": "working", "code": 0, "uri": "https://nemoarchive.org/", "info": ""} +{"filename": "programming/SSH-SWC-cluster.md", "lineno": 266, "status": "working", "code": 0, "uri": "https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh", "info": ""} {"filename": "index.md", "lineno": 5, "status": "working", "code": 0, "uri": "https://neuroinformatics.dev", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 588, "status": "working", "code": 0, "uri": "https://neuroinformatics.dev/", "info": ""} -{"filename": "open_science/Licensing.md", "lineno": 51, "status": "working", "code": 0, "uri": "https://joinup.ec.europa.eu/collection/eupl/solution/joinup-licensing-assistant/jla-compatibility-checker", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 49, "status": "working", "code": 0, "uri": "https://neuroblueprint.neuroinformatics.dev/", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 64, "status": "working", "code": 0, "uri": "https://gin.g-node.org/", "info": ""} {"filename": "open_science/Data-sharing.md", "lineno": 72, "status": "working", "code": 0, "uri": "https://openneuro.org/", "info": ""} -{"filename": "open_science/Data-sharing.md", "lineno": 77, "status": "redirected", "code": 301, "uri": "https://senselab.med.yale.edu/ModelDB/", "info": "https://modeldb.science/"} -{"filename": "open_science/Data-sharing.md", "lineno": 34, "status": "working", "code": 0, "uri": "https://rdr.ucl.ac.uk/The_Sainsbury_Wellcome_Centre", "info": ""} -{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 131, "status": "working", "code": 0, "uri": "https://sleap.ai/guides/choosing-models.html#", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 177, "status": "working", "code": 0, "uri": "https://sleap.ai/_images/topdown_approach.jpg", "info": ""} +{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 131, "status": "working", "code": 0, "uri": "https://sleap.ai/guides/choosing-models.html#", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 458, "status": "working", "code": 0, "uri": "https://sleap.ai/guides/merging.html", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 439, "status": "working", "code": 0, "uri": "https://sleap.ai/guides/proofreading.html#tracking-method-details", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 34, "status": "working", "code": 0, "uri": "https://rdr.ucl.ac.uk/The_Sainsbury_Wellcome_Centre", "info": ""} +{"filename": "open_science/Licensing.md", "lineno": 13, "status": "redirected", "code": 301, "uri": "https://opensource.org/licenses/BSD-3-Clause", "info": "https://opensource.org/license/bsd-3-clause/"} +{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 131, "status": "working", "code": 0, "uri": "https://sleap.ai/guides/troubleshooting-workflows.html", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 129, "status": "working", "code": 0, "uri": "https://sleap.ai/guides/remote.html#remote-training", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 541, "status": "working", "code": 0, "uri": "https://sleap.ai/installation.html#testing-that-things-are-working", "info": ""} -{"filename": "open_science/Licensing.md", "lineno": 13, "status": "redirected", "code": 301, "uri": "https://opensource.org/licenses/BSD-3-Clause", "info": "https://opensource.org/license/bsd-3-clause/"} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 457, "status": "working", "code": 0, "uri": "https://sleap.ai/tutorials/assisted-labeling.html", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 169, "status": "working", "code": 0, "uri": "https://sleap.ai/tutorials/initial-training.html#training-options", "info": ""} -{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 124, "status": "working", "code": 0, "uri": "https://sleap.ai/tutorials/initial-labeling.html", "info": ""} -{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 131, "status": "working", "code": 0, "uri": "https://sleap.ai/guides/troubleshooting-workflows.html", "info": ""} +{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 73, "status": "working", "code": 0, "uri": "https://sleap.ai/installation.html#conda-package", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 77, "status": "redirected", "code": 301, "uri": "https://senselab.med.yale.edu/ModelDB/", "info": "https://modeldb.science/"} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 124, "status": "working", "code": 0, "uri": "https://sleap.ai/tutorials/new-project.html", "info": ""} -{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 299, "status": "working", "code": 0, "uri": "https://slurm.schedmd.com/sacct.html", "info": ""} +{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 124, "status": "working", "code": 0, "uri": "https://sleap.ai/tutorials/initial-labeling.html", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 238, "status": "working", "code": 0, "uri": "https://slurm.schedmd.com/sbatch.html", "info": ""} +{"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 299, "status": "working", "code": 0, "uri": "https://slurm.schedmd.com/sacct.html", "info": ""} {"filename": "data_analysis/HPC-module-SLEAP.md", "lineno": 288, "status": "working", "code": 0, "uri": "https://slurm.schedmd.com/squeue.html", "info": ""} -{"filename": "open_science/Data-sharing.md", "lineno": 76, "status": "working", "code": 0, "uri": "http://ccdb.ucsd.edu/home", "info": ""} {"filename": "programming/Troubleshooting.md", "lineno": 16, "status": "working", "code": 0, "uri": "https://support.github.com/contact?tags=rr-forks&subject=Detach%20Fork&flow=detach_fork", "info": ""} {"filename": "open_science/Licensing.md", "lineno": 21, "status": "redirected", "code": 301, "uri": "https://tldrlegal.com/", "info": "https://www.tldrlegal.com/"} -{"filename": "open_science/Data-sharing.md", "lineno": 28, "status": "working", "code": 0, "uri": "https://www.doi.org/", "info": ""} -{"filename": "programming/SSH-SWC-cluster.md", "lineno": 273, "status": "working", "code": 0, "uri": "https://www.jetbrains.com/pycharm/", "info": ""} {"filename": "programming/SSH-SWC-cluster.md", "lineno": 273, "status": "working", "code": 0, "uri": "https://www.jetbrains.com/help/pycharm/remote-development-overview.html", "info": ""} -{"filename": "open_science/Data-sharing.md", "lineno": 49, "status": "working", "code": 0, "uri": "https://www.nwb.org/", "info": ""} -{"filename": "open_science/Data-sharing.md", "lineno": 44, "status": "working", "code": 0, "uri": "https://www.ebi.ac.uk/bioimage-archive/", "info": ""} -{"filename": "open_science/Licensing.md", "lineno": 54, "status": "working", "code": 0, "uri": "https://www.imperial.ac.uk/research-and-innovation/support-for-staff/scholarly-communication/research-data-management/sharing-data/research-software/", "info": ""} +{"filename": "programming/SSH-SWC-cluster.md", "lineno": 273, "status": "working", "code": 0, "uri": "https://www.jetbrains.com/pycharm/", "info": ""} {"filename": "open_science/Data-sharing.md", "lineno": 68, "status": "working", "code": 0, "uri": "https://idr.openmicroscopy.org/", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 28, "status": "working", "code": 0, "uri": "https://www.doi.org/", "info": ""} +{"filename": "open_science/Licensing.md", "lineno": 54, "status": "working", "code": 0, "uri": "https://www.imperial.ac.uk/research-and-innovation/support-for-staff/scholarly-communication/research-data-management/sharing-data/research-software/", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 49, "status": "working", "code": 0, "uri": "https://www.nwb.org/", "info": ""} {"filename": "open_science/Data-sharing.md", "lineno": 66, "status": "working", "code": 0, "uri": "https://www.v2.opensourcebrain.org/", "info": ""} -{"filename": "open_science/Data-sharing.md", "lineno": 54, "status": "unchecked", "code": 0, "uri": "mailto:adam.tyson@ucl.ac.uk", "info": ""} {"filename": "index.md", "lineno": 5, "status": "working", "code": 0, "uri": "https://www.sainsburywellcome.org/web/", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 54, "status": "unchecked", "code": 0, "uri": "mailto:adam.tyson@ucl.ac.uk", "info": ""} +{"filename": "open_science/Data-sharing.md", "lineno": 44, "status": "working", "code": 0, "uri": "https://www.ebi.ac.uk/bioimage-archive/", "info": ""} +{"filename": "index.md", "lineno": 5, "status": "working", "code": 0, "uri": "https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit", "info": ""} {"filename": "open_science/Licensing.md", "lineno": 7, "status": "working", "code": 0, "uri": "https://www.ucl.ac.uk/", "info": ""} {"filename": "open_science/Data-sharing.md", "lineno": 62, "status": "working", "code": 0, "uri": "https://zenodo.org/", "info": ""} -{"filename": "index.md", "lineno": 5, "status": "working", "code": 0, "uri": "https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit", "info": ""} diff --git a/output.txt b/output.txt index 62d367d..43f0f40 100644 --- a/output.txt +++ b/output.txt @@ -1,6 +1,6 @@ open_science/Data-sharing.md:42: [redirected permanently] http://www.brainimagelibrary.org/ to https://www.brainimagelibrary.org/ open_science/Data-sharing.md:63: [redirected permanently] https://datadryad.org to https://datadryad.org/stash open_science/Data-sharing.md:65: [redirected permanently] https://ebrains.eu/service/share-data to https://www.ebrains.eu/data/share-data/ -open_science/Data-sharing.md:77: [redirected permanently] https://senselab.med.yale.edu/ModelDB/ to https://modeldb.science/ open_science/Licensing.md:13: [redirected permanently] https://opensource.org/licenses/BSD-3-Clause to https://opensource.org/license/bsd-3-clause/ +open_science/Data-sharing.md:77: [redirected permanently] https://senselab.med.yale.edu/ModelDB/ to https://modeldb.science/ open_science/Licensing.md:21: [redirected permanently] https://tldrlegal.com/ to https://www.tldrlegal.com/